Amino acids structural classification

Neural networks have been applied to IR spectrum interpreting systems in many variations and applications. Anand [108] introduced a neural network approach to analyze the presence of amino acids in protein molecules with a reliability of nearly 90%. Robb and Munk [109] used a linear neural network model for interpreting IR spectra for routine analysis purposes, with a similar performance. Ehrentreich et al. [110] used a counterpropagation network based on a strategy of Novic and Zupan [111] to model the correlation of structures and IR spectra. Penchev and co-workers [112] compared three types of spectral features derived from IR peak tables for their ability to be used in automatic classification of IR spectra. 

The structures and abbreviations for the 20 amino acids commonly found in proteins are shown in Figure 4.3. All the amino acids except proline have both free a-amino and free a-carboxyl groups (Figure 4.1). There are several ways to classify the common amino acids. The most useful of these classifications is based on the polarity of the side chains. Thus, the structures shown in Figure 4.3 are grouped into the following categories (I) nonpolar or hydrophobic... 

See also Skin entries Dermaseptin(s), 18 254, 263-265 amino acid sequence of, 18 2641 properties of, 18 264 Dermaseptin derivatives, 18 266 Dermatan sulfates, 4 706 20 457 classification by structure, 4 723t Dermatin sulfate, 4 98 Dermatitis... 

Table 10.2 Classification of amino acids based on chemical structure...

About 20 species of amino acids are incorporated into polypeptides. The aaRSs that catalyze the formation of the corresponding aa-tRNAs are derived from two precursors that have no evolutionary linkage, as evidenced mostly by the fact that their structures have completely different topologies. and by phylogenetic analyses of the sequences of their amino acid residues. " This classification is also consistent with the differences observed in the interactions of these enzymes with modified substrates and in their reactions with reactive groups mounted on substrate analogues. ... 

Let s go back to the classification of the amino acid side chains (chapter 10). Several of these are hydrocarbons greasy, fat-like side chains. Look at the side chains of leucine, isoleucine, valine, and phenylalanine as examples. Eats and water do not mix. Eats are termed hydrophobic, water-hating. It follows that these side chains will try to do what they can to get out of contact with water. The obvious way to do this is to hide in the center of the protein structure, where they may enjoy the company of like-minded amino acid side chains and avoid that of water molecules—sort of a molecular ethnic cleansing. 

The amino acids that are included in the genetic code (see p.248) are described as proteinogenic. With a few exceptions (see p. 58), only these amino acids can be incorporated into proteins through translation. Only the side chains of the 20 proteinogenic amino acids are shown here. Their classification is based on the chemical structure of the side chains, on the one hand, and on their polarity on the other (see p. 6). The literature includes several slightly different systems for classifying amino acids, and details may differ from those in the system used here. 

In this section, enzymes in the EC 2.4. class are presented that catalyze valuable and interesting reactions in the field of polymer chemistry. The Enzyme Commission (EC) classification scheme organizes enzymes according to their biochemical function in living systems. Enzymes can, however, also catalyze the reverse reaction, which is very often used in biocatalytic synthesis. Therefore, newer classification systems were developed based on the three-dimensional structure and function of the enzyme, the property of the enzyme, the biotransformation the enzyme catalyzes etc. [88-93]. The Carbohydrate-Active enZYmes Database (CAZy), which is currently the best database/classification system for carbohydrate-active enzymes uses an amino-acid-sequence-based classification and would classify some of the enzymes presented in the following as hydrolases rather than transferases (e.g. branching enzyme, sucrases, and amylomaltase) [91]. Nevertheless, we present these enzymes here because they are transferases according to the EC classification. 

The use of enzymes and whole cells as catalysts in organic chemistry is described. Emphasis is put on the chemical reactions and the importance of providing enantiopure synthons. In particular kinetics of resolution is in focus. Among the topics covered are enzyme classification, structure and mechanism of action of enzymes. Examples are given on the use of hydrolytic enzymes such as esterases, proteases, lipases, epoxide hydrolases, acylases and amidases both in aqueous and low-water media. Reductions and oxidations are treated both using whole cells and pure enzymes. Moreover, use of enzymes in sngar chemistiy and to prodnce amino acids and peptides are discnssed. 

Proanthocyanidins and Procyanidins - In a classical study Bate-Smith ( ) used the patterns of distribution of the three principal classes of phenolic metabolites, which are found in the leaves of plants, as a basis for classification. The biosynthesis of these phenols - (i) proanthocyanidins (ii) glycosylated flavonols and (iii) hydroxycinnamoyl esters - is believed to be associated with the development in plants of the capacity to synthesise the structural polymer lignin by the diversion from protein synthesis of the amino-acids L-phenylalanine and L-tyro-sine. Vascular plants thus employ one or more of the p-hydroxy-cinnarayl alcohols (2,3, and 4), which are derived by enzymic reduction (NADH) of the coenzyme A esters of the corresponding hydroxycinnamic acids, as precursors to lignin. The same coenzyme A esters also form the points of biosynthetic departure for the three groups of phenolic metabolites (i, ii, iii), Figure 1. 

Classification In accordance with the structure of the R-group. the amino adds of primary importance can be classified into eight groups. Additional amino acids composing protein are not included in this classification, because they occur infrequently. See Table 4. 

---